Latest update

2025-04-09

Data Source

The data used for this project is from Yang et al., 2019: Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency.

  • Table S2: Temporal Proteomic Data (0min, 30min, 1h, 6h, 12h, 24h, 36h, 48h, and 72h)
  • Table S3: Temporal Transcriptomic (RNA-Seq) Data (0min, 1h, 6h, 12h, 24h, 36h, 48h, and 72h)

For the purpose of our project we realigned the count data for the transcriptomic data with the M11 mouse genome using STAR.

Proteome Data Head
UniprotID GeneID X0m X1h X6h X12h X24h X36h X48h X72h log2FC_0m_1h log2FC_1h_6h log2FC_6h_12h log2FC_12h_24h log2FC_24h_36h log2FC_36h_48h log2FC_48h_72h
Q8R3W2 0610009B22Rik 22.88820 22.58756 22.85770 22.71333 22.49104 22.28791 22.55330 22.90905 -0.3006400 0.2701394 -0.1443739 -0.22229103 -0.20312630 0.2653944 0.35574601
Q9DCS2 0610011F06Rik 25.81078 26.28141 26.05348 25.91008 25.43775 24.96838 24.84230 25.63992 0.4706273 -0.2279365 -0.1433905 -0.47233934 -0.46936564 -0.1260783 0.79762014
Q8BHG2 0610037L13Rik 28.65140 28.39190 28.52414 28.30400 28.25237 28.33117 28.45998 28.38369 -0.2595007 0.1322361 -0.2201394 -0.05162924 0.07879782 0.1288167 -0.07629738
V9GXF1 1110065P20Rik 24.46039 25.00402 24.59935 24.25717 24.35595 24.73614 24.76269 25.85162 0.5436275 -0.4046702 -0.3421763 0.09878239 0.38018522 0.0265473 1.08893786
Q8WUR0 1600014C10Rik 24.30800 23.75634 24.58228 25.11048 24.86278 25.11902 24.71790 23.50057 -0.5516615 0.8259393 0.5282067 -0.24770351 0.25624078 -0.4011161 -1.21733005
J3QMC0 1700003H04Rik 22.82848 24.14460 23.35124 23.62545 23.32869 23.17345 23.28715 NA 1.3161250 -0.7933624 0.2742035 -0.29675879 -0.15523247 0.1136942 NA
Transcriptome Data Head
original_id X0h_rep1 X0h_rep2 X1h_rep1 X1h_rep2 X6h_rep1 X6h_rep2 X12h_rep1 X12h_rep2 X24h_rep1 X24h_rep2 X36h_rep1 X36h_rep2 X48h_rep1 X48h_rep2 X72h_rep1 X72h_rep2 version ensembl_base gene_biotype mgi_symbol
ENSMUSG00000121438.1 486 535 599 526 971 975 790 801 941 847 886 581 414 629 99 161 1 ENSMUSG00000121438 lncRNA
ENSMUSG00000109644.3 41 32 60 44 62 45 101 84 112 110 98 97 31 36 41 41 3 ENSMUSG00000109644 lncRNA 0610005C13Rik
ENSMUSG00000108652.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 ENSMUSG00000108652 lncRNA 0610006L08Rik
ENSMUSG00000086714.3 12 23 14 21 21 21 19 26 20 26 33 23 30 61 50 71 3 ENSMUSG00000086714 lncRNA 0610009E02Rik
ENSMUSG00000043644.6 49 34 69 66 38 34 53 41 56 62 62 43 41 66 103 91 6 ENSMUSG00000043644 lncRNA 0610009L18Rik
ENSMUSG00000020831.19 33 27 34 55 48 41 65 63 57 81 70 65 47 60 83 73 19 ENSMUSG00000020831 protein_coding 0610010K14Rik
TF Prot-RNA-LFC-Ratio Over Time
RNA Binding Protein Target Motifs Enriched in ToD Candidates

The Nono protein is a multifunctional DNA- and RNA-binding protein involved in various nuclear processes:

  • Binding: Binds both double-stranded and single-stranded DNA/RNA.
  • Splicing and Paraspeckles: Involved in pre-mRNA splicing and the formation of nuclear paraspeckles, often in a complex with SFPQ.
  • DNA Repair: Plays a role in DNA repair processes like non-homologous end joining (NHEJ).
  • Transcription Regulation: Regulates transcription by interacting with promoters and enhancers.
  • Circadian Rhythm: Modulates the circadian clock by repressing CLOCK-BMAL1 activity.
  • Synaptic Function: Important for GABAergic synapse organization and synaptic RNA regulation.
  • Neuronal Differentiation: Influences neuronal differentiation through epigenetic modifications.
  • Immune Response: Participates in innate immune responses to DNA viruses.

Nucleolin is a predominant nucleolar protein in growing eukaryotic cells, primarily associated with intranucleolar chromatin and pre-ribosomal particles. Its key functions include:

  • Chromatin Decondensation: Induces chromatin decondensation by binding to histone H1.
  • Ribosome Assembly: Plays a role in pre-rRNA transcription and ribosome assembly.
  • Transcriptional Elongation: May be involved in the process of transcriptional elongation.
  • RNA Binding: Binds RNA oligonucleotides with 5’-UUAGGG-3’ repeats more tightly than telomeric single-stranded DNA with 5’-TTAGGG-3’ repeats.

This protein is a key component of messenger ribonucleoprotein particles (mRNPs) and plays a crucial role in the regulation of germ cell mRNA stability and translation. Its functions include:

  • mRNA Binding: Binds full-length mRNA with high affinity in a sequence-independent manner and binds short RNA sequences with low affinity.
  • Y-box Interaction: Binds to the Y-box consensus promoter element, potentially marking mRNAs for cytoplasmic storage.
  • Cytoplasmic Retention: Essential for the cytoplasmic retention of maternal mRNAs.
  • mRNA Storage: May link transcription and mRNA storage/translational delay by marking specific mRNAs for cytoplasmic storage.

This gene encodes a subunit of the U1 snRNP (small nuclear ribonucleic particle), one of at least five snRNPs to comprise the spliceosome, which functions in processing of pre-mRNAs. The U1 snRNP has been shown to be important in defining the 5’ splice site. Alternative splicing results in multiple transcript variants

This protein is a component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes which provide the substrate for the processing events that pre-mRNAs undergo before becoming functional, translatable mRNAs in the cytoplasm.

Enables RNA binding activity. Involved in several processes, including cell cycle switching, mitotic to meiotic cell cycle; meiotic nuclear division; and spermatid differentiation. Acts upstream of or within mRNA stabilization and trophectodermal cell differentiation. Located in cytoplasm and nucleus. Is expressed in central nervous system; craniocervical region bone; dorsal root ganglion; lung; and rib. Orthologous to human RBM46

Splicing factor, which binds the consensus motif 5’-C[ACU][AU]C[ACU][AC]C-3’ within pre-mRNA and promotes specific exons inclusion during alternative splicing. Interaction with YTHDC1, a RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, promotes recruitment of SRSF3 to its mRNA-binding elements adjacent to m6A sites within exons. Also functions as an adapter involved in mRNA nuclear export. Binds mRNA which is thought to be transferred to the NXF1-NXT1 heterodimer for export (TAP/NXF1 pathway); enhances NXF1-NXT1 RNA-binding activity. Involved in nuclear export of m6A-containing mRNAs via interaction with YTHDC1: interaction with YTHDC1 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export

This protein is a member of the eIF2 complex, playing a crucial role in the early steps of protein synthesis and stress response. Key functions include:

  • Protein Synthesis Initiation: Forms a ternary complex with GTP and initiator tRNA, binding to the 40S ribosomal subunit to form the 43S pre-initiation complex, and later the 80S initiation complex after GTP hydrolysis.
  • GTP/GDP Exchange: Requires GDP-GTP exchange, catalyzed by eIF2B, for recycling and initiating another round of protein synthesis.
  • Integrated Stress Response (ISR): Phosphorylation by stress-sensing kinases turns eIF2-alpha into an inhibitor of global protein synthesis, reducing cap-dependent translation while promoting translation of ISR-specific mRNAs like ATF4 and QRICH1.
  • Mitophagy Activation: Acts as an activator of mitophagy in response to mitochondrial damage by relocating to the mitochondrial surface upon phosphorylation, triggering PRKN-independent mitophagy.
  • DNA and RNA Binding: Enables sequence-specific DNA binding at RNA polymerase II cis-regulatory regions and binds pre-mRNA introns.
  • Regulatory Roles: Involved in positively regulating protein import into the nucleus, circadian rhythm, and protein stability.
  • RNA Splicing: Acts upstream of or within RNA splicing processes.
  • Localization and Expression: Located in the nucleus and expressed in various structures, including the central nervous system, heart, genitourinary system, branchial arch, and early conceptus.
  • Research and Disease Study: Used in studies related to Grn-related frontotemporal lobar degeneration with TDP-43 inclusions, amyotrophic lateral sclerosis type 10, and frontotemporal dementia.
  • Human Orthologs: The human ortholog, TARDBP, is implicated in Parkinson’s disease, amyotrophic lateral sclerosis, and motor neuron disease.
  • RNA Binding: Predicted to enable RNA binding activity.
  • Circadian Regulation: Involved in the circadian regulation of gene expression and the entrainment of the circadian clock by photoperiod.
  • Translation Regulation: Plays a role in the regulation of translation.
  • Gene Expression: Acts upstream of or within the positive regulation of gene expression.
  • Cellular Localization: Predicted to be located in the cytosol and nucleoplasm and active in nuclear specks.
  • Complex Participation: Predicted to be part of a protein-containing complex.
  • Expression: Expressed in various systems, including the alimentary, brain, cardiovascular, genitourinary, and hemolymphoid systems.

Predicted to enable RNA binding activity and identical protein binding activity. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in brain; cortical plate; spinal cord; and trigeminal ganglion

  • Alternative Splicing: Involved in alternative pre-mRNA splicing, particularly activating splicing of exons with weak 5’ splice sites followed by a U-rich stretch, including its own pre-mRNA and TIA1 mRNA.
  • RNA Preference: Shows a preference for binding uridine-rich RNAs.
  • Exon Inclusion: Promotes the inclusion of exon 5 in TIA1, leading to the production of the long isoform (isoform a) of TIA1.
  • Stress Granules Formation: Plays a role in forming cytoplasmic stress granules, acting downstream of stress-induced EIF2S1/EIF2A phosphorylation to recruit untranslated mRNAs to these granules.
  • RNA Binding: Binds to the cytoplasmic polyadenylation element (CPE), a uridine-rich sequence in the mRNA 3’-UTR, causing a conformational change similar to the Venus fly trap mechanism.
  • ER Stress Response: Regulates the activation of the unfolded protein response (UPR) during ER stress in the liver by maintaining the translation of CPE-regulated mRNAs when global protein synthesis is inhibited.
  • Cell Cycle and Cytokinesis: Essential for cell cycle progression, particularly cytokinesis and chromosomal segregation.
  • Oncogenic Role: Acts as an oncogene by promoting tumor growth and progression through the positive regulation of t-plasminogen activator/PLAT translation.
  • Melanocyte Proliferation: Stimulates the proliferation of melanocytes.
  • Synaptic Plasticity: Unlike CPEB1 and CPEB3, it does not play a role in synaptic plasticity, learning, and memory.
  • Gene Transcription and Tumor Suppression: Binds to and stimulates transcription from the TXNIP gene promoter, potentially playing a role in tumor suppression. When associated with SAFB, it also stimulates transcription from the SREBF1 promoter.
  • mRNA Association: Associates with nascent mRNAs transcribed by RNA polymerase II and is part of the supraspliceosome complex, influencing pre-mRNA alternative splice site selection.
  • Alternative Splicing: Can activate or suppress exon inclusion; works with TRA2B to promote exon 7 inclusion in SMN2 and represses the splicing of MAPT/Tau exon 10.
  • RNA Binding: Binds preferentially to single-stranded 5’-CC[A/C]-rich RNA sequence motifs and likely binds RNA as a homodimer. It also binds non-specifically to pre-mRNAs.
  • Cytoplasmic Role: Involved in cytoplasmic TNFR1 trafficking, promoting IL-1-beta-mediated cleavage of TNFR1 ectodomains and the release of TNFR1 in exosome-like vesicles.
  • Binding Specificity: Prefers binding to oligo dC and also binds poly(rC) and poly(rU).
  • Antiviral Signaling Regulation: Acts as a negative regulator of antiviral signaling, specifically by:
  • MAVS Signaling: Serving as an adapter between MAVS and the E3 ubiquitin ligase ITCH, facilitating MAVS ubiquitination and degradation.
  • cGAS-STING Pathway: Interacting with CGAS to prevent the formation of liquid-like droplets necessary for CGAS activation.
  • Erythropoiesis: Along with PCBP1, it is required for erythropoiesis, possibly through the regulation of mRNA splicing.

Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be involved in epithelial structure maintenance. Predicted to be located in Golgi apparatus. Predicted to be active in cytoplasm. Is expressed in Meckel’s cartilage; chondrocranium; and olfactory epithelium.

Nucleotide Content in 5’ UTRs of ToD candidates vs all 5’ UTRs
Nucleotide Content in 3’ UTRs of ToD candidates vs all 3’ UTRs